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Millar lab Models page

We are very grateful to the BioModels team for curating our clock models, in SBML and other formats. New models are also available from our PlaSMo portal. PlaSMo has much additional information and files attached, e.g. different model formats, saved parameter files for mutants, corrections etc.

Most of the models are also listed in Andrew's Research Outputs on the Edinburgh Research Explorer, listed as Other Contributions.

Models of plant circadian clocks and outputs (starch, photoperiod sensors, etc)

bulletModified versions of the Ostreococcus tauri clock model (original is PLM_7) from Dixon et al. New Phytologist (2014), each fixing one light input then re-optimising to fit all the data, in PlaSMo only, PLM_83 to PLM_92, with Copasi versions attached.
bulletSBML models of starch degradation in PlaSMo: Models PLM_77, PLM_78, PLM_79 are models 1, 2, 3 from Seaton, D. D., Ebenhöh, O., Millar, A. J. & Pokhilko, A. (2014) Regulatory principles and experimental approaches to the circadian control of starch turnover. Journal of the Royal Society Interface. 11, 91, p. 20130979. doi: 10.1098/rsif.2013.0979.
bullet MODEL1209110002 is the Pokhilko et al. BMC Sys Bio 2013 model of the Arabidopsis circadian clock, which we term P2012, also available from PlaSMo as PLM_49 from Arabidopsis_clock_2012_TOC1_repressor
bulletThe photoperiod pathway model of Song et al. Science 2012 uses real-time data inputs so it cannot easily be rendered in SBML, so it is not yet available except as Matlab files - please contact Andrew.millar@ed.ac.uk
bullet BIOMD0000000412 is the Pokhilko et al. Mol. Syst. Biol. 2012 model of the Arabidopsis circadian clock, which we term P2011, also available from PlaSMo as PLM_64 from Arabidopsis_clock_P2011. Note: minor errors in published supplementary information are documented here; the published SBML files are correct.
bullet BIOMD0000000273 is the Pokhilko et al. Mol. Syst. Biol. 2010 model of the Arabidopsis circadian clock, which we term P2010, also available from PlaSMo as PLM_6 from Arabidopsis_clock_extend. Note: minor errors in published supplementary information are documented here; the published SBML files are correct.
bullet MODEL1005050000 is the original version in Biomodels of the photoperiod pathway model 3 that controls flowering time in Salazar et al. Cell 2009. Note that this model also contains a version of the interlocking-loop clock model, BIOMD0000000055.
Model 3  of Salazar et al. Cell 2009 is also available from PlaSMo as PLM_9, from here Salazar2009_FloweringPhotoperiod.
All the timeseries data used to constrain the models, and the Matlab files of all the models in the paper, are available from the PlaSMo record as a .ZIP archive. 
bullet BIOMD0000000089 is the Arabidopsis 3-loop clock model, from Locke et al. Mol Syst Biol 2006, which we term L2006.
bullet BIOMD0000000055 is the Arabidopsis interlocking loop clock model, from Locke et al. Mol Syst Biol 2005, which we term L2005b.
bulletThe three main Arabidopsis models of Locke et al. 2005-2006 were also documented and implemented in our Circadian Modelling simulation software, see the Software pages. Only runs in Windows, obsolescent since we have the Input Signal Step Function in SBML.

Other models

bullet MODEL1107230000 is the single-loop clock model for Ostreococcus, from Troein et al. Plant Journal 2011. This is also available, with a Copasi file, from PlaSMo as PLM_7, here.
bullet MODEL0911120000 is the phytochrome-based, synthetic light switch in yeast of Sorokina et al. J. Biol. Eng. 2009.
bullet BIOMD0000000214 is the temperature-compensated Neurospora clock model (model2) of Akman et al. Mol. Syst. Biol. 2008. Model 1 of that paper is MODEL8306248909 in the uncurated branch.

 

bulletMore recent models may be on the Uncurated models page at Biomodels database.

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